If it's legal configuration under federal law it's legal under NY law unless you live in NYC or some other jurisdiction where they have passed an AW ban.
[url]http://a.www.state.ny.us/governor/press/year00/aug9_00.htm[/url]
Assault Weapons Ban: Effective on November 1, 2000
The new law also establishes criminal sanctions for the possession and sale of assault weapons and large capacity ammunition feeding devices in New York State. Since 1994, federal law has restricted the possession of assault weapons and large capacity ammunition clips. [b]This measure mirrors the federal provisions and definitions of "assault weapon" and "large capacity ammunition feeding device," as well as the exclusions and exemptions applicable to each.[/b]
As a result of this legislation, State prosecutors will now be able to prosecute the possession and sale of assault weapons. It will be a Class D violent felony to possess either an assault weapon or a large capacity ammunition feeding device, and a Class D felony to unlawfully sell an assault weapon or large capacity ammunition clip that was [b]manufactured after September 14, 1994.[/b]

So in a nutshell "Yes," As long as you don't alter the AR with such things as a telescoping stock, change the barrel/upper so the barrel can accept any type of supressor, or have a magazine with a date stamped after September, 1994 and/or stamped "For Law Enforcement Only."
Again, make sure local laws, such as in NYC, dont prohibit the gun. Otherwise you have a rifle, not an "Assault Rifle"